FMO DATABASE

FMODB ID: 5J8RZ

Calculation Name: 3BPQ-B-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3BPQ

Chain ID: B

ChEMBL ID:
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UniProt ID: P0CL56

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-635909.966506
FMO2-HF: Nuclear repulsion	600953.458737
FMO2-HF: Total energy	-34956.507769
FMO2-MP2: Total energy	-35061.287654

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(B:3:VAL)

Summations of interaction energy for fragment #1(B:3:VAL)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-13.182	-4.363	9.66	-5.565	-12.911	-0.017

Interaction energy analysis for fragmet #1(B:3:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : 0.001

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	B	5	PHE	0	0.007	-0.010	2.407	-1.938	0.964	1.023	-1.405	-2.520	0.004
4	B	6	ALA	0	0.004	0.016	6.231	-0.037	-0.037	0.000	0.000	0.000	0.000
5	B	7	LYS	1	1.012	0.978	9.876	-0.089	-0.089	0.000	0.000	0.000	0.000
6	B	8	THR	0	-0.002	-0.003	12.830	-0.024	-0.024	0.000	0.000	0.000	0.000
7	B	9	PHE	0	0.085	0.060	7.964	-0.008	-0.008	0.000	0.000	0.000	0.000
8	B	10	VAL	0	0.041	0.020	10.264	-0.033	-0.033	0.000	0.000	0.000	0.000
9	B	11	LYS	1	0.897	0.953	12.313	-0.080	-0.080	0.000	0.000	0.000	0.000
10	B	12	ASP	-1	-0.713	-0.822	13.451	0.111	0.111	0.000	0.000	0.000	0.000
11	B	13	LEU	0	0.003	-0.005	10.491	-0.018	-0.018	0.000	0.000	0.000	0.000
12	B	14	LYS	1	0.878	0.924	14.078	-0.013	-0.013	0.000	0.000	0.000	0.000
13	B	15	HIS	0	0.011	0.026	17.554	-0.009	-0.009	0.000	0.000	0.000	0.000
14	B	16	VAL	0	-0.031	0.009	14.470	0.003	0.003	0.000	0.000	0.000	0.000
15	B	17	PRO	0	0.025	0.023	17.554	-0.012	-0.012	0.000	0.000	0.000	0.000
16	B	18	GLY	0	0.068	0.017	17.467	-0.005	-0.005	0.000	0.000	0.000	0.000
17	B	19	HIS	0	0.052	0.021	16.868	-0.021	-0.021	0.000	0.000	0.000	0.000
18	B	20	ILE	0	-0.005	-0.003	15.149	-0.013	-0.013	0.000	0.000	0.000	0.000
19	B	21	ARG	1	0.946	0.967	12.997	0.059	0.059	0.000	0.000	0.000	0.000
20	B	22	LYS	1	0.969	0.991	12.069	0.108	0.108	0.000	0.000	0.000	0.000
21	B	23	ARG	1	0.960	0.976	12.585	0.038	0.038	0.000	0.000	0.000	0.000
22	B	24	ILE	0	0.019	0.010	8.756	-0.017	-0.017	0.000	0.000	0.000	0.000
23	B	25	LYS	1	0.917	0.951	8.079	0.418	0.418	0.000	0.000	0.000	0.000
24	B	26	LEU	0	-0.008	-0.005	8.096	-0.116	-0.116	0.000	0.000	0.000	0.000
25	B	27	ILE	0	-0.065	-0.025	6.167	0.034	0.034	0.000	0.000	0.000	0.000
26	B	28	ILE	0	0.018	-0.004	2.766	-0.752	-0.093	0.120	-0.130	-0.650	0.001
27	B	29	GLU	-1	-0.829	-0.913	3.779	-1.939	-1.507	0.006	-0.158	-0.280	-0.001
28	B	30	GLU	-1	-0.857	-0.889	6.340	-0.905	-0.905	0.000	0.000	0.000	0.000
29	B	31	CYS	0	-0.031	0.003	2.738	0.302	-1.706	4.709	-0.721	-1.979	0.001
30	B	32	GLN	0	-0.075	-0.038	2.691	-3.825	-1.536	0.967	-1.069	-2.188	-0.008
31	B	33	ASN	0	-0.083	-0.056	3.531	0.377	0.307	0.026	0.269	-0.224	0.000
32	B	34	SER	0	0.029	-0.002	6.277	0.184	0.184	0.000	0.000	0.000	0.000
33	B	35	ASN	0	-0.055	-0.021	3.625	-0.351	0.237	0.005	-0.168	-0.425	-0.001
34	B	36	SER	0	-0.036	-0.010	4.972	0.719	0.767	-0.001	-0.001	-0.045	0.000
35	B	37	LEU	0	-0.025	-0.049	5.078	-0.126	-0.126	0.000	0.000	0.000	0.000
36	B	38	ASN	0	-0.040	-0.039	8.071	0.089	0.089	0.000	0.000	0.000	0.000
37	B	39	ASP	-1	-0.834	-0.890	11.709	-0.094	-0.094	0.000	0.000	0.000	0.000
38	B	40	LEU	0	0.002	0.010	8.775	0.007	0.007	0.000	0.000	0.000	0.000
39	B	41	LYS	1	0.929	0.980	11.305	0.290	0.290	0.000	0.000	0.000	0.000
40	B	42	LEU	0	-0.056	-0.044	9.054	0.001	0.001	0.000	0.000	0.000	0.000
41	B	43	ASP	-1	-0.730	-0.825	13.820	0.052	0.052	0.000	0.000	0.000	0.000
42	B	44	ILE	0	0.007	-0.010	9.684	0.024	0.024	0.000	0.000	0.000	0.000
43	B	45	LYS	1	0.918	0.950	13.689	-0.119	-0.119	0.000	0.000	0.000	0.000
44	B	46	LYS	1	0.937	0.980	14.694	-0.205	-0.205	0.000	0.000	0.000	0.000
45	B	47	ILE	0	-0.045	-0.019	15.303	-0.034	-0.034	0.000	0.000	0.000	0.000
46	B	48	LYS	1	0.955	0.973	17.739	-0.081	-0.081	0.000	0.000	0.000	0.000
47	B	49	GLY	0	0.053	0.018	21.164	-0.003	-0.003	0.000	0.000	0.000	0.000
48	B	50	TYR	0	0.026	0.027	17.541	-0.001	-0.001	0.000	0.000	0.000	0.000
49	B	51	HIS	0	0.071	0.032	16.716	-0.017	-0.017	0.000	0.000	0.000	0.000
50	B	52	ASN	0	-0.036	-0.027	12.056	-0.048	-0.048	0.000	0.000	0.000	0.000
51	B	53	TYR	0	0.027	0.022	11.876	0.043	0.043	0.000	0.000	0.000	0.000
52	B	54	TYR	0	0.023	0.003	10.429	-0.083	-0.083	0.000	0.000	0.000	0.000
53	B	55	ARG	1	0.784	0.881	12.221	-0.069	-0.069	0.000	0.000	0.000	0.000
54	B	56	ILE	0	0.034	0.026	8.520	-0.020	-0.020	0.000	0.000	0.000	0.000
55	B	57	ARG	1	0.862	0.931	12.869	-0.033	-0.033	0.000	0.000	0.000	0.000
56	B	58	VAL	0	-0.026	-0.022	12.541	-0.022	-0.022	0.000	0.000	0.000	0.000
57	B	59	GLY	0	0.012	0.008	15.775	-0.004	-0.004	0.000	0.000	0.000	0.000
58	B	60	ASN	0	0.010	-0.009	19.580	0.013	0.013	0.000	0.000	0.000	0.000
59	B	61	TYR	0	-0.002	-0.006	16.088	0.004	0.004	0.000	0.000	0.000	0.000
60	B	62	SER	0	-0.035	-0.024	15.294	-0.007	-0.007	0.000	0.000	0.000	0.000
61	B	63	ILE	0	-0.005	0.007	8.582	-0.006	-0.006	0.000	0.000	0.000	0.000
62	B	64	GLY	0	-0.003	0.001	11.643	-0.014	-0.014	0.000	0.000	0.000	0.000
63	B	65	ILE	0	-0.007	-0.011	6.185	0.009	0.009	0.000	0.000	0.000	0.000
64	B	66	GLU	-1	-0.773	-0.855	8.286	0.488	0.488	0.000	0.000	0.000	0.000
65	B	67	VAL	0	0.019	0.007	7.165	0.193	0.193	0.000	0.000	0.000	0.000
66	B	68	ASN	0	0.002	0.005	7.706	-0.307	-0.307	0.000	0.000	0.000	0.000
67	B	69	GLY	0	0.005	0.002	9.223	0.147	0.147	0.000	0.000	0.000	0.000
68	B	70	ASP	-1	-0.832	-0.918	8.395	0.564	0.564	0.000	0.000	0.000	0.000
69	B	71	THR	0	-0.018	-0.004	4.189	0.302	0.470	0.000	-0.025	-0.142	0.000
70	B	72	ILE	0	0.000	0.017	2.352	-2.181	-1.011	1.104	-0.531	-1.743	0.000
71	B	73	ILE	0	-0.003	0.000	2.587	-1.442	0.098	1.226	-1.342	-1.423	-0.015
72	B	74	PHE	0	0.041	0.007	2.729	-1.823	-0.722	0.475	-0.284	-1.292	0.002
73	B	75	ARG	1	0.826	0.872	6.358	-0.655	-0.655	0.000	0.000	0.000	0.000
74	B	76	ARG	1	0.757	0.828	9.981	-0.205	-0.205	0.000	0.000	0.000	0.000
75	B	77	VAL	0	-0.034	-0.016	11.290	0.022	0.022	0.000	0.000	0.000	0.000
76	B	78	LEU	0	0.020	0.020	13.267	-0.020	-0.020	0.000	0.000	0.000	0.000
77	B	79	HIS	0	0.040	0.017	17.069	0.002	0.002	0.000	0.000	0.000	0.000
78	B	80	ARG	1	0.974	0.960	20.032	-0.026	-0.026	0.000	0.000	0.000	0.000
79	B	81	LYS	1	0.937	0.966	21.952	-0.014	-0.014	0.000	0.000	0.000	0.000
80	B	82	SER	0	0.034	0.020	21.580	-0.003	-0.003	0.000	0.000	0.000	0.000
81	B	83	ILE	0	-0.052	-0.029	18.487	0.008	0.008	0.000	0.000	0.000	0.000
82	B	84	TYR	0	0.003	-0.001	21.639	0.005	0.005	0.000	0.000	0.000	0.000
83	B	85	ASP	-1	-0.846	-0.913	24.249	0.054	0.054	0.000	0.000	0.000	0.000
84	B	86	TYR	0	-0.071	-0.031	20.257	0.008	0.008	0.000	0.000	0.000	0.000
85	B	87	PHE	0	-0.025	-0.015	23.655	0.009	0.009	0.000	0.000	0.000	0.000
86	B	88	PRO	0	0.021	0.031	26.168	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:3:VAL)